To evaluate the avian influenza virus (AIV) circulation in Antarctic and sub-Antarctic penguins we carried out a serosurvey on six species from Livingston, Marion and Gough islands. Seropositivity against AIV was performed on serum samples using a competitive enzyme-linked immunosorbent assay and haemagglutination and neuraminidase inhibition assays. Some oropharyngeal and cloacal swabs were also assayed to detect influenza virus genomes by real time reverse transcription-polymerase chain reaction. Overall, 12.1% (n = 140) penguins were seropositive to AIV. By species, we detected 5% (n = 19) and 11% (n = 18) seroprevalence in sub-Antarctic rockhopper penguins (Eudyptes spp.) from Gough and Marion islands, respectively, 42% (n = 33) seroprevalence in macaroni penguins (Eudyptes chysolophus Brandt), but no positives in the three other species, gentoo (Pygoscelis papua Forster; n = 25) and chinstrap penguins (P. antarctica Forster; n = 16), from Livingston Island and king penguins (Aptenodytes patagonicus Miller; n = 27) from Marion Island. While seropositivity reflected previous exposure to the AIV, the influenza genome was not detected. Our results indicate that AIV strains have circulated in penguin species in the sub-Antarctic region, but further studies are necessary to determine the precise role that such penguin species play in AIV epidemiology and if this circulation is species (or genus) specific.

As a result of the recent application of DNA based technology to the investigation of maritime Antarctic freshwater lakes, patterns have begun to emerge in the bacterioplankton communities that dominate these systems. In this study, the bacterioplankton communities of five Antarctic and five Arctic freshwater lakes were assessed and compared with existing data in the literature, to determine whether emerging patterns in Antarctic lakes also applied to Arctic systems. Such a bipolar comparison is particularly timely, given the current interest in biogeography, the global distribution of microorganisms and the controversy over the global ubiquity hypothesis. In addition, it has recently been discovered that commonly encountered bacterial sequences, often originating from uncultivated bacteria obtained on different continents, form coherent phylogenetic freshwater clusters. In this study we encountered both identical sequences and sequences with a high degree of similarity among the bacterioplankton in lake water from both poles. In addition, Arctic freshwater lakes appeared to be dominated by some of the same groups of bacterioplankton thought to be dominant in Antarctic lakes, the vast majority of which represented uncultivated groups.

Fortyeight freshwater algae (excluding Cyanophyceae) were identified from nine lakes and pools at Hope Bay (Antarctic Peninsula). The geographic distribution in Antarctica and the ecological characteristics of the sampling sites are given for each taxa. Sixteen of them, new records for Antarctica, are described and illustrated. Among the algal classes treated here, Bacillariophyceae and Chlorophyceae constitute the most diverse groups. Most of the species found have been recorded from Antarctica, and many of them are widespread. Some degree of polymorphism was observed in Bacillariophyceae and Tribophyceae taxa.

The diet of the Antarctic blue-eyed shag Phalacrocorax atriceps bransfieldensis was analysed based on the identification of the prey items in 50 regurgitated casts collected at Duthoit Point, Nelson Island, in February 1991. Fish remains occurred in 100% of the casts and represented 68% by number and 90% by weight of the total prey items. From a total of 2112 otoliths found, 1176 fish specimens were identified belonging to four demersalbenthic species: Harpagifer antarcticus, Notothenia neglecta, Nototheniops nudifrons and Trematomus newnesi. Equations to estimate total length and weight from otolith length are provided. H. antarcticus and N. neglecta were the most frequent (92%) and important by weight (66%) respectively. Cephalopod beaks found indicate benthic octopods as the second group in importance after fish. Other invertebrates such as polychaetes, gastropods, bivalves and crustaceans were only occasional. The presence of algae and stones in the casts is attributed to accidental ingestion. Our results are in general agreement with those published for other Antarctic localities which indicate that P. atriceps is a benthic coastal feeder, with fish as its main food.

Palmaria decipiens (Reinsch) R.W. Ricker (1987) represents one of the dominant rhodophyte species in Antarctic coastal ecosystems. Due to its high abundance in the intertidal and upper subtidal it plays a key role in ecosystem structure and function, providing habitat, food and shelter for a multitude of associated organisms. The physiology, reproductive strategy and life cycle of P. decipiens is considered as being well adapted to the Antarctic environment, which is characterized by permanent low water temperatures and a strong seasonality in light climate. With its obvious ecological significance and adaptive strategies P. decipiens was frequently studied as a typical representative of an endemic Antarctic macroalga. Here we provide an overview of the recent literature, summarizing the knowledge gained about the alga during the last 25 years. This review focuses on the species life cycle and physiological responses, such as temperature requirements, photosynthetic characteristics, pigment content and protective mechanisms with regard to enhanced ultraviolet radiation (UV-B radiation, 280–315 nm and UV-A radiation, 315–400 nm). The ecology of P. decipiens is reviewed focussing on grazing activity and abundance patterns. Since most studies on P. decipiens have been conducted at King George Island off the western Antarctic Peninsula this overview serves as a summary of baseline data from an ecosystem particularly prone to environmental change.

Polychaetes, the dominant macrofaunal taxa of the Antarctic soft sediments, provided more than 40% of the animals found in Martel Inlet. However, little information is available on the composition of meiofaunal communities in polar areas. This study identified the meiofaunal polychaete species and described their bathymetric distribution in the nearshore zone. Sediment cores were taken by divers from 6–25 m depth in the summer of 1991 and 1994 in front of the Brazilian Antarctic Station (Martel Inlet, Admiralty Bay). Additional sampling was done at the 18 m depth in 1994 in order to study the influence of ice scouring. A total of 1895 specimens in 17 families were found. Three species (Apistobranchus glacierae, Leitoscoloplos kerguelensis and Ophryotrocha notialis), all of them belonging to the temporary meiofauna, provided more than 70% of the total polychaete fraction. This meiofaunal component showed similar distributional patterns to those of the macrofaunal polychaetes in this area.

The Scotia Arc and Amundsen Sea are contrasting regions within West Antarctica. The Scotia Sea shelf is well studied and central to the origin and diversity of the Southern Ocean benthic fauna, whilst the shelf of Amundsen Sea is one of the least studied shelf areas in the world; a ‘white spot’ on the map of benthic research. Here we report on the tanaidaceans collected using an epibenthic sledge on two expeditions, BIOPEARL 1 and 2, of the RRS James Clark Ross in 2006 and 2008, respectively. This study represents the first analysis of the tanaidacean fauna of those two basins. Thirty-seven species were found in the Amundsen Sea from 500–1500 m depth and 51 species were found at depths ranging from 200–1600 m in the Scotia Sea. In the Scotia Sea, many species were unique to each of the study sites which may be evidence of allopatric speciation episodes. Site specificity was especially evident for Typhlotanais and Pseudotanais. Only three species were common to both basins. Around 90% of the species were previously undescribed. Our findings increase the number of the tanaidaceans known in the Southern Ocean by 50%.

Epiphytic diatoms are important constituents of the Southern Ocean coastal water ecosystem, being a key element in many of the Antarctic trophic chains. However, only limited information exists relating to these microalgal communities. Here we describe our findings of a study on epiphytic diatoms from Terra Nova Bay (Ross Sea, Antarctica) based on material collected during the summer campaigns spanning from 1990–2004. Observations of diatoms associated with three rhodophyte species (Iridaea cordata (Turner) Bory, Phyllophora antarctica Gepp & Gepp, and Plocamium cartilagineum (L.) Dixon) were carried out with the use of a scanning electron microscope. A total of 73 diatom taxa (32 genera) were distinguished, of which 20 taxa exceeded 3% of total abundance. Cocconeis fasciolata (Ehrenberg) Brown, Navicula perminuta Grunow, and Fragilariopsis nana (Steemann Nielsen) Paasche appeared in every sample. The analysis of similarities (ANOSIM) test as well as non-metric multidimensional scaling analysis indicated the nature of host organism as a major factor influencing associated diatom community structure, whereas depth, site, and time of sampling seemed to be less important. The epizooic communities associated with sessile fauna epiphytic on macroalgae differed significantly from those associated with macroalgal surface. A pronounced difference between the communities epiphytic on various host macroalgae species was also observed, although most of the dissimilarities occurred between diatom taxa of the same growth form.

The arrival of iceberg B09B in Commonwealth Bay, East Antarctica, and subsequent fast ice expansion has dramatically increased the distance Adélie penguins (Pygoscelis adeliae) breeding at Cape Denison must travel in search of food. This has provided a natural experiment to investigate the impact of iceberg stranding events and sea ice expansion along the East Antarctic coast. As part of the Australasian Antarctic Expedition 2013–14, the Adélie penguin colony at Cape Denison was censused to compare to historic counts. Whilst some 5520 pairs still bred at Cape Denison there has been an order of magnitude decline in Adélie numbers in the area in comparison to the first counts a century ago and, critically, recent estimates based on satellite images and a census in 1997. In contrast, an Adélie population on the eastern fringe of Commonwealth Bay just 8 km from the fast ice edge was thriving, indicating the arrival of B09B and fast ice expansion was probably responsible for the observed recent population decline. In conclusion, the Cape Denison population could be extirpated within 20 years unless B09B relocates or the now perennial fast ice within the bay breaks out. Our results have important implications for wider East Antarctic if the current increasing sea ice trend continues.

We have sequenced the 18S–26S nuclear ribosomal DNA ITS region from the genome of nine different moss species from the Ross Sea region of Antarctica. This relatively quick and simple technique enables these species to be readily distinguished, facilitating their taxonomic identification. Only a single moss shoot is required, and for identification of these bryophytes it is only necessary to determine a few hundred nucleotides of the DNA sequence in a single sequencing reaction. Several previously unidentified Antarctic moss specimens were readily characterized by comparison with ITS sequences of known moss species. The relationships between species and locations previously detected by the RAPD (Random Amplified Polymorphic DNA) technique were confirmed by DNA sequencing, demonstrating that the two techniques can be complementary for molecular analysis of the ecology of mosses in Antarctica.

The effect of solar radiation on the survival of Escherichia coli, Salmonella zanzibar and a faecal Streptococcus strain in seawater was tested in laboratory experiments, and survival of E. coli was tested under natural light conditions at Davis Station, Antarctica. Exposure to artificial light of wavelengths 290–800 nm caused a rapid decline in viability of each strain examined. T90 values (the time taken for 90% of the population to be inactivated) were ~50 min, 40 min and 2 h for E. coli, S. zanzibar and the faecal Streptococcus respectively. Selective removal of UV-B wavelengths of (<320 nm) increased survival of E. coli and S. zanzibar, resulting in T90 values of ~2.5 h. Screening out wavelengths of <370 nm (UV-B and most of UV-A) increased T90 values to 5 h for E. coli and 10 h for S. zanzibar. The visible band of the spectrum (400–800 nm) also had deterimental effects on faecal bacteria, when compared with survival in the absence of light. Rates of decline for E. coli in natural light in Antarctica were similar to those from laboratory experiments. However, resuscitation of sub-lethally damaged cells under optimum conditions resulted in greater recovery rates than were observed after exposure to artificial sunlight. Faecal bacteria were rapidly inactivated when exposed to sunlight in Antarctic waters, and as repair mechanisms are unlikely to operate under in situ conditions, resuscitation of sub-lethally damaged cells is improbable.

Soil chronosequences in till deposits emplaced during glacial retreat in the Central Transantarctic Mountains are described. Discrepancies between the degree of soil development and reported cosmogenic surface exposure ages suggest slower, weaker soil development in this region than encountered in other areas of Antarctica. The study sites (Dominion Range, Mount Achernar and Ong Valley) were located between 83° and 85°S, at altitudes of 1600–2200 m, on the edge of the polar plateau. Soil landscape maps show a gradation of soil properties across landscape units that were designated as homogenous/single-event drifts in previous smaller-scale studies. Along transects away from the current ice edge, the depth to underlying ice thickened (from 2 cm to > 80 cm), soil became more weathered, saltier and less alkaline, and horizonation became more pronounced. Soil thickness, clast abundance and soil chemistry are all consistent with a two-layer mode of soil formation. We suggest that a thin, clast-rich surface horizon, originating from weathering of supraglacial debris, overlies a thick, clast-poor sublimation till. The supraglacial debris has a finite contribution to soil volume, whereas sublimation offers an ongoing source of soil material that thickens the soil from its base.

The capacity of the polar flora to adapt is of increasing concern given current and predicted environmental change in these regions. Previous genetic studies of Antarctic mosses have been of limited value due to a lack of variation in the markers or non-specificity of the methods used. We examined the power of five microsatellite loci developed for the cosmopolitan moss Ceratodon purpureus to detect genetically distinct clones and infer the distribution of clones within and among populations from the Windmill Islands, East Antarctica. Our microsatellite data suggest that the extraordinarily high levels of variation reported in RAPD studies were artificially elevated by the presence of contaminants. We found surprisingly little contribution of asexual reproduction to the genetic structure of the Windmill Islands populations, but more loci are required to determine the distribution of individual clones within and among populations. It is apparent that Antarctic populations of C. purpureus possess less genetic diversity than temperate populations, and thus have less capacity for adaptive change in response to environmental variation, but more markers are needed to resolve the total genetic diversity in Antarctic C. purpureus and other mosses.

The liquid soil water contents in the seasonally thawed layer (active layer) were characterized from seven soil climate monitoring sites - four coastal sites from south to north (Minna Bluff, Scott Base, Marble Point and Granite Harbour), and inland sites from low to high altitude (Wright Valley, Victoria Valley and Mount Fleming). Mean water contents ranged from 0.013 m3 m-3 near the surface at Victoria Valley to 0.33 m3 m-3 near the ice-cemented layer at Granite Harbour. The coastal sites have greater soil water contents than the McMurdo Dry Valley and Mount Fleming sites, and moisture contents increase with depth in the active layer. The Wright Valley site receives very little infiltration from snowmelt, with none in most years. All other sites, except Mount Fleming, received between one and four wetting events per summer, and infiltrated water moved to greater depths (≈ 10–25 cm). The Scott Base and Granite Harbour sites are on sloping ground and receive a subsurface flow of water along the ice-cemented permafrost. Our findings indicate that water contents are low with very little recharge, are greatly influenced by the local microclimate and topography, and show no significant increasing or decreasing trend over 10 years of monitoring.

Bacterial community composition during summer was analysed in surface and bottom waters of the oligotrophic shallow (4.5 m) Lake Limnopolar (Livingston Island, South Shetland Islands, Antarctica), using 16S rRNA gene clone libraries and sequencing. Up to 61% of the 16S rDNA sequences found were closely related to sequences retrieved from lakes, glaciers or polar systems. The distribution of these sequences was not homogeneous, with vertical differences found in both bacterial taxa composition and isolation source of the closest match from GenBank. In the surface sample 86% of the sequences were related to bacteria found in soils, seawater or gut microbiota, probably explained by waterborne transport from the catchment, by wind through sea sprays, or local bird activity. Conversely, in the deep samples, 95% of the sequences were closer to bacteria typically described for lakes, glaciers or polar systems. The presence of benthic mosses covering the bottom of the lake favours a more stable deep layer leading to the existence of this biological heterogeneity through the water column, although the lake does not show physical-chemical stratification in summer. This study illustrates a strong influence of external factors on the microbial ecology of this model Antarctic lake.

Fixed-point and probabilistic sampling designs were compared to investigate which design best detected known contamination gradients in the marine ecosystem adjacent to McMurdo Station, Antarctica. The fixed-point sampling design included transects along historical contamination and physical disturbance gradients. The probabilistic sampling design used randomly selected hexagons spaced at 50 m intervals. In both designs, 15 stations were sampled over a small area (~1 km2) that extended from Winter Quarters Bay to Cape Armitage. Sediment quality triad components (sediment chemical contaminants, sediment toxicity, and a benthic index of biotic integrity) were measured to indicate chemical, toxicological, and biological effects. There were higher correlations between sediment quality triad components for the fixed-point sampling design than for the probabilistic design. The fixed-point design was better at detecting the intensity of alteration because disturbance of the marine ecosystem at McMurdo Station is localized within a small area. Based on these results, a limited fixed-point design with nine stations detected no significant change in macrofaunal community structure over a four year period from 2000–2004. However, the macrofaunal assemblages present in the contaminated portions of Winter Quarters Bay are indicative of a disturbed benthic community that has been subject to organic enrichment and toxic chemical exposure.

The identities of the 12 lichenicolous fungi described as new to science from the Antarctic and sub-Antarctic islands by Carroll W. Dodge between 1938 and 1968 are reassessed on the basis of the original publications, and where extant the original collections and slides in the Farlow Herbarium and Reference Library (Harvard University, Cambridge, MA, USA). Typifications are discussed and lectotypes and neotypes designated as necessary. Only one species is accepted in its original placement (Phacopsis usneae) and one had already been transferred to an appropriate genus (Didymella cladoniae to Zwackhiomyces). Six prove to be synonyms of previously described species, and four are combined into other genera here: Arthonia parmeliae (syn. Diplonaevia parmeliae), Carbonea antarctica (syn. Alectoria antarctica), Sphaerellothecium buelliae (syn. Orbicula buelliae), and Weddelomyces gasparriniae (syn. Phaeospora gasparriniae) combs. nov. The generic name Thelidiola is also confirmed as a synonym of Muellerella. In addition, as a result of earlier misinterpretations of Dodge’s taxa, two new species are described: Endococcus matzeri, and Zwachkiomyces diederichii spp. nov. Intralichen lichenum is also reported from the Antarctic for the first time. Descriptions and illustrations are included where appropriate.

Available information about seabird breeding population trends on Stinker Point (Elephant Island, Maritime Antarctic Peninsula) is outdated by decades. This study reports current numbers of breeding species, and evaluates population trends over 28 years. We counted breeding pairs of seabirds along all ice-free areas on Stinker Point during two distinct periods (summers of 1985/86–1991/92 and 2009/10–2013/14). Thirteen species currently breed in the area: four Sphenisciformes, four Procellariiformes, one Suliforme and four Charadriiformes. Chinstrap penguin Pygoscelis antarcticus has the highest number of breeding pairs (4971±590), followed by gentoo penguin Pygoscelis papua (1242±339). Comparisons between the two intervals showed declining trends for almost all breeding populations, although southern giant petrels Macronectes giganteus are experiencing a subtle population growth. Population decreases in locations with low human disturbance, such as Stinker Point, may indicate sensibility to climate and environmental change and need further investigation.

In certain regions of the Southern Ocean, tidal energy is believed to foster the mixing of different water masses, which eventually contribute to the formation of deep and bottom waters. The Ross Sea is one of the major ventilation sites of the global ocean abyss and a region of sparse tidal observations. We investigated M2 tidal dynamics in the Ross Sea using a three-dimensional sigma coordinate model, the Regional Ocean Model System (ROMS). Realistic topography and hydrography from existing observational data were used with a single tidal constituent, the semi-diurnal M2. The model fields faithfully reproduced the major features of the tidal circulation and had reasonable agreement with ten existing tidal elevation observations and forty-two existing tidal current measurements. The differences were attributed primarily to topographic errors. Internal tides were generated at the continental shelf/slope break and other areas of steep topography. Strong vertical shears in the horizontal velocities occurred under and at the edges of the Ross Ice Shelf and along the continental shelf/slope break. Estimates of lead formation based on divergence of baroclinic velocities were significantly higher than those based on barotrophic velocities, reaching over 10% at the continental shelf/slope break.

Eight hundred photosynthesis-irradiance relationships were determined in the shelf waters adjacent to Palmer Station, Antarctica during the spring/summer periods of 1991–94. Biomass specific maximum photosynthetic rate, PBmax, and the light limited photosynthetic efficiency, αB, were poorly correlated to the physical forcing and nutrient regimes at the sampling stations. The two photosynthetic parameters, however, did strongly covary indicating the minimum irradiance required to saturate photosynthesis, Ik, was relatively constant in this highly variable environment. The variability in Ik could partially be attributed to both depth in the water column and time of the year, with the highest values occurring for surface samples during the summer period of peak incident irradiance. Given this and the significant dependence of Pmax on phytoplankton biomass, a simple empirical model for primary productivity was developed. An independent test of the model was performed on data collected in a mesoscale offshore grid and predicted primary production was found to be within 13% of measured values. Although there are limitations to this approach (i.e. exclusion of diel periodicity in photosynthetic response), these results provide relatively robust estimates of daily primary production for the Southern Ocean.